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Bugfix/official naming

Marek Szuba requested to merge bugfix/official_naming into master

Created by: magaliruffier


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    • do not modify code without testing for regression
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Using one or more sentences, describe in detail the proposed changes. The transcript name extension is overwritten every time a new loop is started. This results in all transcripts having -201 as an extension, rather than -201, -202 within the same gene. This bugfix re-establishes the former behaviour.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. All transcripts within the same gene have the same name. This means it is harder to distinguish between transcripts without using the stable ID.


If applicable, describe the advantages the changes will have. Transcripts within the same gene have the same name.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes. Users rely on the transcript name and expect it to be stable, which it is fundamentally not.


Have you added/modified unit tests to test the changes? The whole pipeline was run and results compared with previous run.

If so, do the tests pass/fail? Results are comparable.

Have you run the entire test suite and no regression was detected?

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